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Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics
Department of Molecular Biology and Kellogg School of Science and Technology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. TPC6 La Jolla, CA 92037, USA
Department of Chemistry and Biophysics Program, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109, USA
* Author to whom correspondence should be addressed.
Received: 21 January 2009; in revised form: 23 February 2009 / Accepted: 26 February 2009 / Published: 2 March 2009
Abstract: Exploring the landscape of large scale conformational changes such as protein folding at atomistic detail poses a considerable computational challenge. Coarse-grained representations of the peptide chain have therefore been developed and over the last decade have proved extremely valuable. These include topology-based Gō models, which constitute a smooth and funnel-like approximation to the folding landscape. We review the many variations of the Gō model that have been employed to yield insight into folding mechanisms. Their success has been interpreted as a consequence of the dominant role of the native topology in folding. The role of local contact density in determining protein dynamics is also discussed and is used to explain the ability of Gō-like models to capture sequence effects in folding and elucidate conformational transitions.
Keywords: Protein folding; Gō models; coarse-graining; energy landscape; conformational transitions
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Hills, R.D., Jr.; Brooks, C.L., III Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics. Int. J. Mol. Sci. 2009, 10, 889-905.
Hills RD, Jr, Brooks CL, III. Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics. International Journal of Molecular Sciences. 2009; 10(3):889-905.
Hills, Ronald D., Jr.; Brooks, Charles L., III. 2009. "Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics." Int. J. Mol. Sci. 10, no. 3: 889-905.